The LED is not a reliable indicator of battery status on a bricked kindle. It is controlled by SOFTWARE, not by hardware. In fact, the battery charger is also controlled by SOFTWARE, so bricking a kindle can interfere with charging the battery.

We have had excellent recovery success by charging the battery first. Charge the battery with a wall charger for at least two hours, then use MfgTool to change to fastboot mode (which charges better and faster according to serial i/o messages about battery status during fastboot mode). Charge it in fastboot mode AT LEAST two more hours (preferably overnight) then try again. There are three different people I helped who succeeded ONLY after there battery got enough charge. Without enough, you will see strange behavior, like RUNME.sh not finishing, or fastboot not working, or MfgTool starting to download u-boot to the Kindle but never finishing.

So, charge it enough to get into fastboot mode, then charge it some more. There is a good chance you WILL be able to get to diags, from which you CAN repair you kindle using USB drive export and a custom RUNME.sh launched by data.tar.gz, to fix your "custom" problem...

I have my touch connected to a serial port now, and the ONLY serial i/o messages I see during and after booting to fastboot are battery voltage messages, which show a steady quick charge up to 4.190 volts, where it stabilizes (my k4nt stabilizes at 4.171 volts). Now that I have a good battery charge, I will try debricking it again.

I ONLY see these battery messages while in fastboot mode. In other modes they kindle just aborts my repair attempts faster and faster until it is completely dead and cannot be seen by MfgTool. It does NOT charge on USB in main or diags mode unless on a wall charger, and then not very quickly or reliably.

I think that the reason is because fastboot loads the full bist u-boot from mmc (why there are two u-boot sets above), and the larger bist build has better battery charging code in int. Booting to main or diags just uses the little u-boot that was loaded into RAM.